Analysis of skin pigmentation and genetic ancestry in three subpopulations from pakistan: Punjabi, pashtun, and baloch
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Analysis of skin pigmentation and genetic ancestry in three subpopulations from pakistan : Punjabi, pashtun, and baloch. / Shan, Muhammad Adnan; Meyer, Olivia Strunge; Refn, Mie; Morling, Niels; Andersen, Jeppe Dyrberg; Børsting, Claus.
In: Genes, Vol. 12, No. 5, 733, 05.2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Analysis of skin pigmentation and genetic ancestry in three subpopulations from pakistan
T2 - Punjabi, pashtun, and baloch
AU - Shan, Muhammad Adnan
AU - Meyer, Olivia Strunge
AU - Refn, Mie
AU - Morling, Niels
AU - Andersen, Jeppe Dyrberg
AU - Børsting, Claus
N1 - Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2021/5
Y1 - 2021/5
N2 - Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopula-tion had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10−3). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations.
AB - Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopula-tion had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10−3). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations.
KW - Biogeographic ancestry
KW - Externally visible characteristics
KW - Forensic DNA phenotyping
KW - Pigmentation
KW - Skin color
UR - http://www.scopus.com/inward/record.url?scp=85106859615&partnerID=8YFLogxK
U2 - 10.3390/genes12050733
DO - 10.3390/genes12050733
M3 - Journal article
C2 - 34068188
AN - SCOPUS:85106859615
VL - 12
JO - Genes
JF - Genes
SN - 2073-4425
IS - 5
M1 - 733
ER -
ID: 272186157